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Introducing the Next Generation Biology Workbench, Version 1.0

Published 02/26/2008

The San Diego Supercomputer Center (SDSC) at UC San Diego has announced the release of the Next Generation Biology Workbench, version 1.0. The popular system, code named Swami, is a free Web resource accessed thousands of times per week by scientists and students in bioinformatics, genomics, proteomics, and phylogenetics communities worldwide.

Swami links major molecular biology databases with analysis programs through an easy-to-use Web interface. Searching is integrated with a wide variety of analysis and modeling tools, and is designed to eliminate file format compatibility problems. Swami, which runs on powerful computational resources at SDSC, also offers speed, letting researchers complete within hours complex tasks that once took days, weeks, or even months.

"Swami is designed to put powerful biological analysis tools within easy reach of biology educators, students, and researchers, without the cost of having to install and manage a complex infrastructure," said Mark Miller, Swami project leader at SDSC. "Our goal is to provide services to biologists at institutions of all scales, so the biology research community isn't fragmented into cyber-haves and cyber-have nots."

Funded by the National Institutes of Health (NIH), Swami is based on the original Biology Workbench introduced more than 10 years ago by UCSD bioinformatics pioneer Shankar Subramaniam when he was at the National Center for Supercomputing Applications (NCSA).

The Next Generation Biology Workbench has been re-engineered so that new tools and data types can be added easily. This will help the toolkit grow according to the evolving needs of the community, and make it possible for other developers to contribute tools to the Workbench. The re-engineered workbench also simplifies adding new databases, and makes it possible to easily move the application to other computational resources.

Swami v1.0 features include:

  • Most original Biology Workbench tools, with greater data handling flexibility in the new Swami environment
  • The Sirius protein structure viewer, a full-featured structure and modeling tool that permits creation, display, and overlay of complex model structures
  • Tools from the Phylip Phylogeny Inference Package

Additional features that the development team plans to release in 2008 include an interactive phylogenetic tree viewer, the ability to share data with colleagues within the workbench, and tools for DNA sequence assembly.

A focus of the development team has been to make this advanced tool available to users with all levels of training, from beginning students to advanced researchers, and to make Swami available independent of where users are located and with minimal barriers to entry.

The project team has embraced best practices in software development, focusing on reliable and well-understood technologies that ensure a dependable production resource.

In addition to Miller, Swami team members include Celeste Brown, University of Idaho; and SDSC staff Jin Ruan, Hannes Niedner, Jeremy Carver, Rami Rifaieh, Roger Unwin, and Ashton Taylor.

The Swami team invites user input to help set priorities as the project continues. For more information on Swami visit

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